[Biopython-dev] [Bug 3060] Add ungap method to the SeqRecord?

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jun 22 14:58:39 UTC 2010


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
Attachment #1482 is|0                           |1
           obsolete|                            |

------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-22 10:58 EST -------
(From update of attachment 1482)
(In reply to comment #3)
> I've been trying building SeqFeature objects for the reads in an ACE file,
> http://github.com/peterjc/biopython/tree/ace-reads
> In this case when I call the SeqRecord ungap method, many of my read features
> are lost with the current implementation (because they included gaps). This
> also showed the ungap code to be quite slow for features. I'm going to have
> another look at this.

My new code handles SeqFeature ungapping so as to preserve all the features by
adjusting their end points. This is also much faster:


Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list